Classification of the ECU as Mission Critical Equipment (MCE) which must be located outside of an electromagnetic barrier.
Hardening of the ECU using "Special Protective Measures" as defined in MIL-STD-188-125-2
Maximum re-use of proven HEMP-hardened ECU design
Location of Controls inside EM barrier with appropriate treatment of barrier penetrations
HEMP hardening of MCE, which must be located outside an electromagnetic barrier, is accomplished using "Special Protective Measures" (MIL-STD-188-125-2 Section 4.3.6 and Section 5.8)
Special Protective Measures (SPM) may include:
Use of good EM-reduction layout and construction techniques
Linear and nonlinear transient suppression / attenuation devices
Equipment-level hardening measures
Use of inherently robust technologies and components
Cable, conduit and local volume shielding
Shelter EM barrier Interfaces by fiber optic connection
HEMP set-up and testing is involved and quite detailed.